The "secret" goal of 50 Blessings / the janitors is falseThe stuff on the computer, and the stated goals of the janitors, are false. The janitors really are arranging everything as a big social experiment. 50 Blessings uses the "make America strong" pretext as a way to find people who are willing to kill. Why did the janitors order Rat-Man to attack Jacket? Because they realized that Jacket could seriously have the ability to end the game by destroying the Russian mob, and therefore, ending the whole pretext for the social experiment. Why are the janitors upset that Biker hacked their computer? They're only acting upset and feeding the Biker lies so that the Biker won't know the truth - perhaps the truth would expose some of the backers of the experiment. When they see that the Biker believes them / doesn't care for politics, they can settle on the "make America strong" explanation as the main one. The file that the Biker found on the computer was merely one of the PDFs on the desktop, a brochure that *appeared* to state their goals. It is quite possibly the same brochure that attracted the Biker to sign up for 50 Blessings, but he is such a thrill-seeker that he doesn't even remember reading it before, so when he reads it again, it seems to be new to him. Why do the janitors more-confidently state their true goals to the Biker if he does *not* hack the computer? Because the secrets of the backers of the experiment are safely guarded within the computer. The janitors can say all they want as long as they don't reveal anything substantial. (this theory is mainly to allow the maximum possible room for fan-fiction)
The game is part of the Mondo timelineIt's always fun to theorize! Mondo Medicals - a powerful and influential man tries to fight cancer. Hotline Miami - the man extends his reach into Miami, hoping to develop... let us say... new techniques for battling cancer. Killing cancer on a big scale. Mondo Agency - The leader of Mondo Medicals successfully took over the country and installed a new president. Unfortunately, the cancer is mutating... the parts where everything begins to get increasingly weird is still part of the Hitman's Sanity Slippage, but also represents the Man with the Square-Rimmed Glasses starting to think he isn't up for being part of the program anymore. The part where he is "replaced" with the angry guy refusing to give anything to the Hitman indicates that he is either refusing to pay the Hitman for any more of his jobs, or really was replaced by a far more unsympathetic handler by 50 Blessings.
The masked men in the hitman's dream sequence represent his conscience.The Rooster is himself, telling him what he already knows. The owl represents all the people he's killed, hence why he's scared, hostile, and says he's leaving when the conspiracy is taken down. The horse is a representation of the hitman's girlfriend.
Neither the hitman nor the biker died at Phonehom.The hitman's survived worse than a knife to the chest, and the biker makes it clear (in his side of the story, at least) that he doesn't want to kill the hitman. He probably gave him a No-Holds-Barred Beatdown, kicked him aside, and left.
The Biker put Richard (or Jacket or Hitman, whatever) in the coma.From the Biker's perspective, he ends up bashing in Richard's head and telling him that he warned him. The events in Richard's coma could be in no particular continuity (since the dreams are out of whack anyway), and it might be possible that the police and doctors talked about what happened to his girlfriend while he was in bed, possibly able to comprehend what they said. They never did say that he was shot in the head. Even in Richard's perspective, it looked like Richter shot him in the neck. Inconsistent to how he ended up in a coma.
The game's story is made up of two diverging timlinesThe point of divergency here being whether Jacket or the Biker dies in their confrontation. The game after the fight while playing as Jacket is what happens if Jacket had won the fight, and the post-story chapters with the Biker is if he had won the fight.
The sequel will have a cultist faction.It's been mentioned that there'll be multiple factions involved in the game, and the bonus mission of the original, "Highball," depicted a strange symbol and two men performing a ritualistic sacrifice. Not a huge leap to make.
The Hitman is being forced into killing.In the first mission, he vomits at the end of it, a clear sign of remorse. He goes out of his way to save the girl in the second mission. He always seems a little reluctant to leave his apartment (notice how he moves slower than normal). Moreover, we know that the people that are calling him regularly force compliance with threats. Sure, they're empty threats, but Hitman has no way of knowing that. Notably, when he stops going out based on the answering machine messages, he's much more goal-oriented: revenge against those that tried to kill him. Even the drug-haze can be summed up that way: in order to dull his moral sensibilities, he takes drugs, resulting in the weird style and colors. He doesn't want to kill all these people, but he has no choice: he's been threatened.
The Hitman and the Biker represent the two types of player who play Hotline MiamiThe Hitman represents players who are interested in the story of the game and want to figure out what's going on. They recognize what they are doing is horrible and wrong, and their primary goal of the game is to stop whoever is doing the killings. They don't include themselves as the cause because they were ordered to do it, so they go after whoever's giving the messages on the phone. They are interested in the characters (Hence the recurring characters of the girlfriend and the shopkeeper) and are hit hardest by their departure. The Hitman's apartment and appearance also implies this: his outfit makes sense for the occasion being both practical and reasonable for the era, and his apartment starts out grotty, becomes decidedly more pleasant as the story establishes a pattern, then seriously goes downhill when the third act happens, representing the motions of the story. The Biker represents players who just want to have fun and enjoy the murder. They know they aren't exactly doing morally right things within the game, but they really don't care about that since they enjoy killing and their primary goal is just having fun. They will take the violent route to solving all problems and they only wish to uncover the mystery because that seems to be the only way to end the game and it is seriously dragging on by that point. They know the characters too, but unlike the Hitman they really don't care about them: the women who show up at his apartment are presumably of romantic connection but don't show up again, and the informants he bothers never show up again. Like the Hitman, his outfit and apartment both imply this; his outfit is pretty absurd and garish, and probably intentionally so: ever see what an intentionally ridiculous RPG character/Sim looks like? His apartment is similarly stylized: there is a lot more computers and toys then most people could afford in the 80s, but it looks really damn nice. The funny thing is, neither the Biker nor the Hitman get what they want. The Hitman brutally dispatches the Russian Mafiya's bosses without much emotion, never gets the whole picture, and might have even helped the scheme along even when he was trying to rebel. The Biker dispatches the two janitors without much of a satisfying battle as they don't even fight back, and then rides off in his bike to god knows where, not truly being satisfied by what happened. This makes sense, since the achievement for completing the game is "Was that it?", which probably means both types of players coming away unhappy was the intention.
Everything after "Neighbors" is the Hitman's Dying Dream.